A common reason for the Index Status count to go down at the "update" is that an alternate version of the website is verified in Webmaster Tools. A simple way to double-check that is to do a site:-query for just your domain name (eg https://www.google.com/#q=site:fish.com ), and to see which version is shown. If the www-version is shown, then that's the version where most of your data will be. If you want to be on the safe side, just verify both of them.
Thank youfor the this interesting info... but in my case I have a sub domain which falling down it's index status in GWT and both version of the website is verified by GWT... any idea why?
I'd look at the sitemaps indexed URL count more as a metric, since the index status count can include URLs that you don't really care about. Don't blindly follow any metric, think about where it comes from & consider if it's really what you need to focus on.
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